Variant report

Variant	rs3754535
Chromosome Location	chr2:30368876-30368877
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:30368744-30370075	GM12891	blood:	n/a	n/a
2	BHLHE40	chr2:30368862-30370056	K562	blood:	n/a	n/a
3	BHLHE40	chr2:30368861-30369864	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:30368827-30370102	K562	blood:	n/a	n/a
5	TCF12	chr2:30368862-30370179	A549	lung:	n/a	n/a
6	MAZ	chr2:30368876-30371087	IMR90	lung:	n/a	n/a
7	POLR2A	chr2:30368576-30371359	MCF10A-Er-Src	breast:	n/a	n/a
8	NFYB	chr2:30368769-30369907	GM12878	blood:	n/a	chr2:30369531-30369545
9	CTCF	chr2:30368868-30371293	SK-N-SH	brain:	n/a	chr2:30370307-30370320 chr2:30370308-30370318 chr2:30369319-30369326
10	MXI1	chr2:30368627-30371538	IMR90	lung:	n/a	n/a
11	MXI1	chr2:30368738-30371599	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr2:30368628-30368944	SH-SY5Y	brain:	n/a	chr2:30368876-30368883
13	REST	chr2:30368584-30371302	H1-neurons	neurons:	n/a	chr2:30369549-30369563 chr2:30369595-30369608 chr2:30369551-30369561
14	EP300	chr2:30368805-30369965	GM12878	blood:	n/a	chr2:30369604-30369620
15	MXI1	chr2:30368805-30369956	GM12878	blood:	n/a	n/a
16	CHD1	chr2:30368604-30371625	IMR90	lung:	n/a	chr2:30369572-30369582 chr2:30369567-30369577
17	SP1	chr2:30368871-30370135	HCT-116	colon:	n/a	chr2:30369566-30369576 chr2:30369669-30369681 chr2:30369670-30369679 chr2:30369566-30369576 chr2:30369708-30369720 chr2:30369567-30369576 chr2:30369670-30369680 chr2:30369565-30369577 chr2:30369671-30369680 chr2:30369666-30369680 chr2:30369566-30369575 chr2:30369708-30369720 chr2:30369765-30369777 chr2:30369567-30369576 chr2:30369709-30369719 chr2:30369710-30369719 chr2:30369765-30369777 chr2:30369565-30369577 chr2:30369710-30369719 chr2:30369709-30369718 chr2:30369670-30369680 chr2:30369523-30369544 chr2:30369615-30369626 chr2:30369565-30369576 chr2:30369766-30369775 chr2:30369767-30369776 chr2:30369709-30369719 chr2:30369671-30369680 chr2:30369762-30369776 chr2:30369669-30369681
18	MAX	chr2:30368849-30369944	A549	lung:	n/a	n/a
19	POLR2A	chr2:30368612-30371120	MCF10A-Er-Src	breast:	n/a	n/a
20	FOS	chr2:30368781-30368993	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:30361445..30366413-chr2:30367443..30370864,6	MCF-7	breast:
2	chr2:30368663..30370783-chr2:30453321..30456156,2	K562	blood:
3	chr2:30361415..30365100-chr2:30365958..30368991,4	K562	blood:
4	chr2:30366474..30375732-chr2:30375765..30384167,14	MCF-7	breast:
5	chr2:30363131..30365100-chr2:30367257..30368991,2	K562	blood:
6	chr2:30337518..30339089-chr2:30368226..30369771,2	K562	blood:
7	chr2:30357579..30360858-chr2:30368602..30370618,3	MCF-7	breast:

Variant related genes	Relation type
YPEL5	TF binding region
ENSG00000233862	TF binding region
ENSG00000119801	Chromatin interaction
ENSG00000213626	Chromatin interaction
ENSG00000233862	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1137288	0.82[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs11886753	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12463847	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12469080	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13397907	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13403749	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17009192	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2084335	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3087895	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951983	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4952095	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4952096	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4952098	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4952102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4952105	1.00[ASW][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap]
rs55735005	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59074474	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7567202	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7600457	0.82[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7603324	0.82[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1002657	chr2:30339312-30516535	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv1794716	chr2:30356661-30370785	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30368400-30369000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:30368600-30369000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:30368600-30369000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr2:30368600-30369000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:30368600-30369000	Enhancers	Brain Substantia Nigra	brain
6	chr2:30368600-30369000	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr2:30368600-30369000	Enhancers	Fetal Intestine Small	intestine
8	chr2:30368600-30369000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr2:30368600-30369000	Enhancers	Fetal Muscle Leg	muscle
10	chr2:30368600-30369000	Enhancers	Fetal Stomach	stomach
11	chr2:30368600-30369200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr2:30368600-30369200	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr2:30368600-30369200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr2:30368600-30369200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr2:30368600-30369200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:30368600-30369200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr2:30368600-30369200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr2:30368600-30369200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:30368600-30369200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr2:30368600-30369200	Flanking Active TSS	HMEC	breast
21	chr2:30368600-30369200	Flanking Active TSS	NHEK	skin
22	chr2:30368600-30369400	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr2:30368600-30369400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:30368600-30369400	Flanking Active TSS	GM12878-XiMat	blood
25	chr2:30368600-30370800	Active TSS	Fetal Brain Female	brain
26	chr2:30368600-30371200	Active TSS	Brain Angular Gyrus	brain
27	chr2:30368800-30369000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:30368800-30369000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:30368800-30369000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
30	chr2:30368800-30369000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
31	chr2:30368800-30369000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
32	chr2:30368800-30369000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr2:30368800-30369000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr2:30368800-30369000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:30368800-30369000	Enhancers	Liver	Liver
36	chr2:30368800-30369000	Enhancers	Brain Germinal Matrix	brain
37	chr2:30368800-30369000	Flanking Active TSS	Fetal Brain Male	brain
38	chr2:30368800-30369000	Enhancers	Fetal Heart	heart
39	chr2:30368800-30369000	Enhancers	Fetal Kidney	kidney
40	chr2:30368800-30369000	Enhancers	Fetal Lung	lung
41	chr2:30368800-30369000	Enhancers	Placenta	Placenta
42	chr2:30368800-30369000	Enhancers	Stomach Mucosa	stomach
43	chr2:30368800-30369000	Active TSS	Stomach Smooth Muscle	stomach
44	chr2:30368800-30369000	Flanking Bivalent TSS/Enh	A549	lung
45	chr2:30368800-30369000	Enhancers	HSMM	muscle
46	chr2:30368800-30369000	Active TSS	HSMMtube	muscle
47	chr2:30368800-30369000	Flanking Bivalent TSS/Enh	NH-A	brain
48	chr2:30368800-30369200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:30368800-30369200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:30368800-30369200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell

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